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A raft of recent articles show the strength and versatility of a standardized genetic approach to identifying species, ie DNA barcoding. Just as color vision helps us rapidly sort objects into unambiguous categories, DNA analysis usually reveals distinct differences among species, including those whose biological differences lie outside the range of our perception, ie cryptic species. I highlight two of the recent articles below.

In March 20, 2007 Proc Natl Acad Sci USA, researchers at University of Guelph, Canadian Agricultural Department, and University of Pennsylvania apply DNA barcoding to 16 species of apparently generalist parasitoid tachnid flies. Smith et al found 73 distinct mitochondrial DNA lineages among 2,134 flies from the 16 morphospecies. The mitochondrial lineages were supported by collateral ecological differences and, where tested, by independent nuclear gene markers. In an accompanying commentary, Scott Miller, Smithsonian Institution, looks at how DNA barcoding is contributing to the “renaissance of taxonomy” and is “emerging as a cost-effective standard for rapid species identification”.

In 26 March 2007 Mol Ecol Notes, scientists from the University of Auckland apply DNA to identifying rat species in Southeast Asia. Geographic variation in mitochondrial DNA of commensal rats provides a window into patterns of human dispersal and migration, but studies are complicated by the presence of multiple rat species in Southeast Asia, and the difficulty of distinguishing among species in subfossil remains at archeological sites.  Robins et al found DNA barcoding with COI mtDNA barcodes distinguished most species, even when short DNA fragments of COI were used (such as might be recoverable from sub-fossil material), and was similarly effective as tree-based methods using COI, cytochrome b, and D-loop sequences.  The genetic methods revealed some polytypic and paraphyletic species, suggesting a need for taxonomic revisions in this group.

The biological universe is much larger and more diverse than we thought. In three papers in March 2007 PLoS Biology, scientists report on a genetic survey of microbial diversity in the world’s oceans.  A large collaboration, the Global Oceanic Sampling (GOS), led by Craig Venter, analyzed microbial DNA collected by filtering seawater at 250 sites along a several thousand kilometer transect from the North Atlantic, through the Panama Canal, around the Galapagos Islands, ending in the Cocos Islands of the South Pacific. The resulting DNA dataset consisted of 6.3 billion base pairs (twice the size of the human genome), with 85% of the assembled and 57% of the unassembled data unique at a 98% identity cutoff. The extreme diversity prevented assembly of complete genomes, as many reads were unique. A comprehensive dataset of GOS sequences combined with pre-exisiting databases reveals nearly 6.12 million proteins, nearly doubling the number of known proteins. Some families of microbial proteins discovered in this study, particularly protein kinases, were previously thought to be restricted to eukaryotic organisms. Over 1700 sequence clusters show no identity to known families, implying we are far from knowing the full range of what proteins can do. 

How to make sense of all this data? First, more data is needed!, namely more complete genomes into which the unassembled fragments can be placed. Second, new analytic tools. A new genomics and informatics group based at the California Institute for Telecommunications and Information Technology in San Diego, have built a metagenomics version of GenBank, known as the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (try saying that 3 times quickly!) which is fortunately known by acronym CAMERA. 

Just as Google and other search engines solved a problem of information overload that did not exist a few years ago, I am confident that CAMERA and other new informatics tools will enable us to view the expanding universe of environmental genomics, including DNA barcode libraries, in ways that will provide new understanding.

Over 1000 fish species can be legally sold in the United States, a challenge for accurate labelling. Many fish products such as fillets cannot be identified to species, even by experts. DNA surveys suggest that at least for some expensive species, most fish products are mislabelled. In 2004 Nature 430:309, scientists at University of North Carolina analyzed mtDNA of fish labelled as red snapper, which by US law can only be applied to a Caribbean snapper species, Lutjanus campechanus. 77% (17/22) fish purchased from 9 vendors in eight states were not L. campechanus, and most were species from other regions of the world, or could not be identified to species due to lack of reference sequences.

More recently, the availability of commercial DNA testing has enabled enterprising news stations to do their own research. Last year a Florida television station found that 6 of 11 restaurant entrees labeled as local grouper were other species, including Asian catfish and tilapia, and last month a Los Angeles television station reported that red snapper entrees at 4 local restaurants were either tilapia, catfish, or mahi mahi.  Following up on the news media, the Florida Attorney General’s office did their own testing, found 17 of 24 restaurants sold entrees mislabeled as grouper, and made legal settlements. What is needed is needed is a widely available method backed up by a reliable reference library that can be routinely applied to identification of fish and fish products in the marketplace. DNA barcoding is designed to be just that. 

The Food and Drug Adminstration (FDA) Regulatory Fish Encyclopedia (RFE) aims “to assist with the accurate identification of species and help federal, state, and local officials and purchasers of seafood identify species substitution and economic deception in the marketplace.”

The species pages include scientific and common names, pictures of whole fish and fish products, analytic gels of fish proteins, and excitingly, an empty space for reference DNA sequence information. For reliable identification, the fish reference library needs comprehensive taxonomic coverage and adequate sampling of variation within species, ie DNA barcoding. I believe the Fish Barcode of Life Initiative (Fish-BoL), which has already collected barcodes from over 16,000 specimens representing more than 3500 species, will provide a widely used tool that will benefit consumers and the many species of fish that require management or protection.  

A dozen articles in current issue of Nature examine the legacy of Carl Linnaeus, born 300 years ago this May. The wonderful cover illustration shows Carl Linnaeus as a modern field biologist in blue jeans and down vest, holding up a DNA barcode.  I am particularly struck by Charles Godfray’s “Linnaeus in the information age,” a wide-ranging, thoughtful, visionary and practical look at how taxonomy might evolve so as to provide the widest benefit to society. His near-term wish list includes “a comprehensive web-based taxonomic and identification resource (morphology plus DNA barcodes) for the world’s macrolepidoptera”, which “would be a wonderful lever for bringing new resources into the field.”  A central theme echoed in many of the pieces is the need for taxonomists to join together and create “big science” projects that benefit the many end-users of taxonomic knowledge.